M. Zudi Jasser is a physician, a U.S. Navy veteran, an American patriot and a Muslim who does not hold with those who preach that Islam commands its followers to take part in a war against unbelievers.

The Third Jihad, a documentary film Jasser narrated, takes a hard look at those Muslims who are waging this war – both with bombs and by stealthier means. The film had been among the educational materials used to train New York City police officers concerned with terrorism. Then, last month, The New York Times went on what one might call a crusade against the movie, publishing a series of articles branding it a “hate-filled film about Muslims” and calling on Police Commissioner Raymond Kelly to “apologize for the film … and make clear that his department does not tolerate such noxious and dangerous stereotyping.”

In the first of its stories, the Times charges that the film “casts a broad shadow over American Muslims.” That ignores the unambiguous statement with which the documentary opens: “This is not a film about Islam. It is about the threat of radical Islam. Only a small percentage of the world’s 1.3 billion Muslims are radical.”

The story quotes Jasser as saying in the film: “This is the true agenda of Islam in America.” But what Jasser actually said in the film is that jihad is “the true agenda of much of the Muslim leadership here in America.”

Jasser has long argued – and he’s hardly alone in this -- that the leaders of some of the wealthiest and most powerful organizations that claim to represent American Muslims are not as moderate as they’d have you believe. Prominent among such organizations is CAIR, the Council on American-Islamic Relations, which appears to have been the driving force behind the coverage in the Times and in the Village Voice before that. The Times quotes CAIR spokesmen saying how outraged and offended they are by the film.

The Times does chooses not to inform readers that CAIR was an unindicted co-conspirator in the largest terrorism-financing trial in the U.S. to date, the 2007 US v Holy Land Foundation et al. The Times neglects to report that the FBI has broken all ties with CAIR. The Times also does not mention that last year CAIR’s national organization lost its status as a tax deductible charity after it failed to file required annual reports detailing revenues for three consecutive years as required by law. (The Times has raised pointed questions about funding for The Third Jihad. Why no interest in where CAIR’s money comes from?)

The paper never bothered to interview Jasser. Nor did the Times quote Robert Jackson, the only Muslim on the New York City Council who told other reporters that while he “initially thought from reading about [the film] that it cast a negative image on all Muslims … it does not. It focuses on the extreme Muslims that are trying to hurt other people.” The Times turned down an op-ed by former Secretary of Homeland Security Tom Ridge and former CIA Director (and current chairman of the Foundation for Defense of Democracies) Jim Woolsey defending the film.

The Times’ stories present not a single factual error in the documentary. However, illustrating the first story was an image of the White House with a black Islamic flag flying above it. The Times called that “a doctored photograph,” leaving readers to infer that the filmmakers had done the doctoring. In fact, the filmmakers found that image on a jihadi web site. (Such images are common on such websites as any reporter working the terrorism beat should know.)

CAIR calls itself a Muslim “civil rights” organization and most of the major media take it at its word. Jasser has pointed out that one of the main missions of such groups is to silence critics -- to deprive them of their right to free speech. One of the ways this is done, Jasser says, is by making it appear that Muslim reformers are themselves extremists and, what is more, that they are “not part of the community (ummah), and so subject them to takfir (declaring them apostates). That is what the vicious distortions about this film do to my work and the work of so many others within the House of Islam who are trying to publicly take on the American Islamist establishment.”

Jasser adds: “Political Islam is the lifeblood of groups like CAIR; they will never publicly acknowledge its incompatibility with western liberalism and Americanism. Were Americans ever to finally become educated to the slippery slope between nonviolent Islamism (political Islam) and Islamist militancy, the legitimacy of these Muslim-Brotherhood-legacy groups would evaporate.”

The barriers to providing such education are growing. Mayor Bloomberg has denounced The Third Jihad. The NYPD has stopped showing it. CAIR is not at all satisfied. The organization has demanded that Commissioner Kelly resign and that the police department “offer a concrete plan to help counter the misinformation about Islam and Muslims provided to almost 1500 officers through the screening of The Third Jihad.”

That won’t be the end of it. Author Bruce Bawer noted in an op-ed this week: “Criticizing Islam is now a punishable offense in several European countries.” I happened to have read Bawer’s piece while waiting for a train in New York’s Penn Station. About the same time, I heard an announcement on the public address system: “If you see something, say something.” Zudi Jasser has seen something. CAIR wants him to shut up about it. And CAIR has friends in high places.